Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

Awesome Protein Representation Learning

Generation of protein sequences and evolutionary alignments via discrete diffusion models

:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.

Get protein embeddings from protein sequences

A Python API for the RCSB Protein Data Bank (PDB)

FAPLM: A Drop-in Efficient Pytorch Implementation of Protein Language Models

AbLang: A language model for antibodies

Lbster: Language models for Biological Sequence Transformation and Evolutionary Representation

Neural Networks for Protein Sequence Alignment

Open-source usearch

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. (DEPRECATED)

Inference of couplings in proteins and RNAs from sequence variation

A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design

Affinity Protein-Protein Transformers—State of the art protein-protein binding affinity in seconds!

Multi-task and masked language model-based protein sequence embedding models.

Protein 3D structure prediction pipeline

An R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.

Variational autoencoder for protein sequences - add metal binding sites and generate sequences for novel topologies

Inference code for PoET: A generative model of protein families as sequences-of-sequences

A collection of simple JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. The Sequence Manipulation Suite is commonly used by molecular biologists, for teaching purposes, and for program and algorithm testing.

PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.

LAMBDA – the Local Aligner for Massive Biological DatA

Protein structure alignment and search algorithm

The official code for "TaxDiff: Taxonomic-Guided Diffusion Model for Protein Sequence Generation"

Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

A fully automated gene annotator from RNA-Seq expression data

Paratope Prediction using Deep Learning

Official repository for discrete Walk-Jump Sampling (dWJS)

Official repository for discrete Walk-Jump Sampling (dWJS)